Hi,

I'm trying MAST for differential analysis in a scRNA-seq experiment. I have some experimental and control batches, like "exp1", "exp2", "exp3" and "ctrl1", "ctrl2", and I use Seurat to integrate them and perform clustering. Now I want to find differential expressed genes between experimental and control group for each cluster, but I do not know how to do. I have tried codes like something below, but it didn't work.

zlm.output <- zlm(~ batches, sca.1)
lrTest(zlm, Hypothesis('(exp1+exp2+exp3)/3 - (ctrl2+`Intercept`)/2'))

Any suggestions?

Thanks!